I'm not too sure about this one... but just in case...
Have you ckecked if you can access the items/urls in the folders on the personal toolbar itself? If so maybe they may appear in the folders themselves again.
Another thing I might be inclined to try is to make a new folder in the bookmarks and set
it as the toolbar folder... see if the older folder now has the items in it. If so you could just move everything to this new folder... delete the old one and rename the new folder to something appropriate... I think by default it's just "Personal Toolbar Folder".
And then the "old cautionary note"...
Make a regular recent backup of your User Profile folder so in case these things happen you can swap items from the good backed up one...